Stimulus_sens_1 - PFAM28P - GREMLIN Contacts

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Stimulus_sens_1 - Stimulus-sensing domain

PFAM:	PF13756	Sequences: INPERAAPLLRRLVSPTRTRARLYDRDGRLIADSRNLYGPRGDVLRFDLPPPEEEKPGLLERAYDALRRWLGRGDLPLYRELGPANGKDYPEVARALAGEPASAVRVNERG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	111 (108)
Sequences:	4496 (3073)
Seq/√Len:	295.7
META:	0.927

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
44_V	49_L	4.505	1.00
79_Y	90_Y	3.136	1.00
82_L	89_D	2.963	1.00
6_A	23_L	2.684	1.00
66_A	70_W	2.414	1.00
59_L	63_A	2.338	1.00
87_G	93_V	2.279	1.00
76_L	79_Y	2.190	1.00
64_Y	68_R	2.169	1.00
16_P	21_A	2.088	1.00
86_N	89_D	1.917	1.00
63_A	66_A	1.903	1.00
25_D	29_R	1.878	1.00
14_V	21_A	1.871	1.00
60_L	63_A	1.781	1.00
61_E	65_D	1.663	1.00
45_L	49_L	1.620	1.00
25_D	31_I	1.544	1.00
56_K	60_L	1.506	1.00
99_G	102_A	1.480	1.00
40_P	43_D	1.468	1.00
92_E	106_R	1.444	1.00
68_R	71_L	1.433	1.00
63_A	67_L	1.432	1.00
43_D	47_F	1.400	1.00
10_L	16_P	1.399	1.00
54_E	57_P	1.370	1.00
14_V	17_T	1.340	1.00
95_R	100_E	1.334	1.00
52_P	56_K	1.326	1.00
60_L	64_Y	1.322	1.00
95_R	102_A	1.301	1.00
42_G	46_R	1.281	1.00
9_L	12_R	1.260	1.00
91_P	104_A	1.252	1.00
42_G	45_L	1.221	1.00
41_R	49_L	1.212	1.00
42_G	47_F	1.209	1.00
65_D	68_R	1.208	1.00
38_Y	42_G	1.168	1.00
41_R	45_L	1.152	1.00
14_V	18_R	1.142	1.00
4_E	8_P	1.142	1.00
12_R	15_S	1.140	1.00
45_L	48_D	1.136	1.00
56_K	64_Y	1.117	1.00
13_L	16_P	1.114	1.00
12_R	35_R	1.113	1.00
58_G	61_E	1.069	1.00
62_R	65_D	1.062	1.00
62_R	66_A	1.058	1.00
43_D	46_R	1.056	1.00
34_S	42_G	1.046	1.00
76_L	90_Y	1.035	1.00
10_L	21_A	1.026	1.00
5_R	8_P	1.017	1.00
61_E	64_Y	1.004	1.00
5_R	9_L	0.999	1.00
83_G	88_K	0.999	1.00
56_K	59_L	0.976	1.00
41_R	46_R	0.959	1.00
56_K	65_D	0.948	1.00
7_A	12_R	0.938	1.00
55_E	59_L	0.928	1.00
82_L	85_A	0.927	1.00
63_A	73_R	0.926	1.00
85_A	89_D	0.924	1.00
52_P	55_E	0.921	1.00
99_G	105_V	0.911	1.00
40_P	46_R	0.910	1.00
65_D	69_R	0.896	1.00
36_N	45_L	0.885	1.00
3_P	7_A	0.882	1.00
10_L	14_V	0.877	1.00
42_G	49_L	0.876	1.00
85_A	90_Y	0.854	1.00
7_A	32_A	0.851	1.00
92_E	105_V	0.848	1.00
66_A	69_R	0.829	1.00
59_L	62_R	0.826	1.00
52_P	57_P	0.824	1.00
44_V	48_D	0.820	1.00
61_E	68_R	0.799	1.00
44_V	50_P	0.793	0.99
88_K	94_A	0.787	0.99
13_L	32_A	0.783	0.99
46_R	49_L	0.782	0.99
10_L	41_R	0.780	0.99
26_R	36_N	0.775	0.99
57_P	61_E	0.769	0.99
55_E	58_G	0.761	0.99
16_P	19_T	0.757	0.99
24_Y	30_L	0.753	0.99
13_L	21_A	0.745	0.99
17_T	21_A	0.744	0.99
14_V	19_T	0.743	0.99
81_E	87_G	0.740	0.99
15_S	18_R	0.730	0.99
21_A	92_E	0.719	0.99
55_E	61_E	0.716	0.99
24_Y	85_A	0.716	0.99
20_R	96_A	0.714	0.99
91_P	95_R	0.709	0.99
9_L	26_R	0.709	0.99
20_R	81_E	0.702	0.99
9_L	16_P	0.698	0.99
80_R	88_K	0.698	0.99
104_A	107_V	0.690	0.99
44_V	47_F	0.690	0.99
57_P	68_R	0.689	0.99
46_R	50_P	0.677	0.98
82_L	87_G	0.676	0.98
54_E	58_G	0.665	0.98
24_Y	90_Y	0.663	0.98
8_P	23_L	0.662	0.98
7_A	14_V	0.660	0.98
101_P	104_A	0.656	0.98
56_K	61_E	0.650	0.98
101_P	105_V	0.649	0.98
64_Y	70_W	0.647	0.98
90_Y	93_V	0.640	0.98
56_K	66_A	0.633	0.97
84_P	87_G	0.621	0.97
8_P	31_I	0.619	0.97
94_A	98_A	0.619	0.97
65_D	70_W	0.610	0.97
67_L	70_W	0.609	0.97
72_G	108_N	0.605	0.97
92_E	99_G	0.601	0.97
91_P	94_A	0.601	0.97
70_W	75_D	0.594	0.96
59_L	66_A	0.594	0.96
93_V	99_G	0.589	0.96
79_Y	87_G	0.573	0.95
83_G	86_N	0.573	0.95
10_L	34_S	0.566	0.95
20_R	41_R	0.558	0.95
11_R	42_G	0.556	0.95
66_A	72_G	0.554	0.95
23_L	34_S	0.553	0.95
3_P	8_P	0.552	0.94
38_Y	43_D	0.549	0.94
41_R	47_F	0.548	0.94
81_E	92_E	0.547	0.94
71_L	76_L	0.544	0.94
47_F	50_P	0.542	0.94
18_R	101_P	0.541	0.94
45_L	50_P	0.539	0.94
82_L	88_K	0.536	0.94
9_L	15_S	0.532	0.93
79_Y	89_D	0.531	0.93
59_L	69_R	0.525	0.93
58_G	62_R	0.523	0.93
75_D	78_L	0.515	0.92
7_A	37_L	0.511	0.92
17_T	24_Y	0.509	0.92
11_R	15_S	0.507	0.92
2_N	7_A	0.507	0.92
70_W	76_L	0.505	0.91
81_E	85_A	0.503	0.91
24_Y	87_G	0.503	0.91
63_A	69_R	0.500	0.91

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Prob ≥ 0.7 are listed. For all 3L/2 predictions, click on one of the links below.

Sco = ((raw_sco - min_sco)/(avg_sco - min_sco))/2 + 0.5
Prob = P(contact | Sco, seq80/√len)
seq80 = effective number of sequences, after reducing redundancy to 80% identity

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling
Upload PDB model overlay contacts on the model

HHsearch Results:

Legend: GREMLIN results (Prob ≥ 0.7) overlaid on top PDB hits. The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on the top 10 (or top 20 if e-value < 1E-20) HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.

PDB	Chains	Cov	%	HHΔ
3cwfA	2	0.5495	85.3	0.811	Contact Map
3pjvD	2	0.7387	8.9	0.899	Contact Map
2odaA	2	0.7387	4.6	0.912	Contact Map
3cjyA	2	0.3784	4.5	0.912	Contact Map
2v2fA	1	0.1351	4.5	0.913	Contact Map
3rqbA	2	0.3964	4.4	0.913	Contact Map
3i0uA	1	0.4865	4.3	0.914	Contact Map
1c8uA	2	0.3964	4.3	0.914	Contact Map
3zg9A	1	0.3694	4.1	0.914	Contact Map
4qd8A	3	0.3874	3.9	0.915	Contact Map

Sequence Conservation (Image Generated using WebLogo v3)

Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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